Need Urgent Help, I'm in strange situation

Yesterday, my server's hdd got crashed and the hosting company replaced it with a new hdd and attached the old one to recover data. They installed the new hdd just as a new server, without cpanel or any other changes. Just by installing the Centos 6 x64.

Afterwards, being very less knowledgeable to linux system, I somehow installed cpanel and transferred old files using rsync command. Now, cpanel installed with mysql 5.5, which have default storage system as MyISAM. And, my database tables were in innodb.

Now, I can't downgrade Mysql to 5.1 and unable to change default storage engine as it gives this error upon restarting if i try to change it to Innodb:

Did you have account backups enabled on the system before the hard drive crashed? If so, restoring the accounts through these backup archives is the only supported restoration method. Restoring/moving individual files/directories may work, but you are likely to encounter issues. The manual method is only recommended if you do not have any backup archives to restore.